[gmx-users] centering

[Marc Vogt]

Got around it by making the original pdb file with extra options
in trjconv after seeing the recent post on a similar issue.

trjconv -f wholestar.trr -s test.tpr -b 1110 -e 1110 -pbc inbox -o tsw.pdb -center

thanks,
Marc

> 
> I've read the archives and I've been trying to center a solute
> in a box with solvent and I still can't do it.  I have a pdb file
> from a trajectory that looks something like this:
> 
> 	wwwww
> 	wwwww
> 	 wwppp
> 	wwwww
> 	wwwww
> 
> w is water and p is protein
> 
> I want:
> 
> 	wwwww
> 	wwwww
> 	wpppw
> 	wwwww
> 	wwwww
> 
> 
> The box is 50 Angstroms x 50 Angstroms x 50 Angstroms.
> I tried
> editconf -f start.pdb -o centered.pdb -center 2.5 2.5 2.5
> and 
> editconf -f start.pdb -o centered.pdb -c
> 
> and different versions of gromacs but the resulting centered.pdb always 
> looks like the starting one.  Seems like it should be easy and I'm sure
> it's something stupid, but I can't get it.
> 
> thanks,
> Marc
>   
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